From 94332596940fbf7d0892b16af593c3fca956b206 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 11 Mar 2020 09:44:34 +0100
Subject: [PATCH] add parameter_meta
---
gatk.wdl | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gatk.wdl b/gatk.wdl
index 0ccf519..b730cbe 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -960,6 +960,8 @@ task HaplotypeCaller {
contamination: {description: "Equivalent to HaplotypeCaller's `-contamination` option.", category: "advanced"}
outputMode: {description: "Specifies which type of calls we should output. Same as HaplotypeCaller's `--output-mode` option.",
category: "advanced"}
+ emitRefConfidence: {description: "Whether to include reference calls. Three modes: 'NONE', 'BP_RESOLUTION' and 'GVCF'",
+ category: "advanced"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
pedigree: {description: "Pedigree file for determining the population \"founders\"", category: "common"}
--
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